https://github.com/noamteyssier/faiquery

perform interval queries on an indexed fasta file
https://github.com/noamteyssier/faiquery

fai fasta indexed-fasta query

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perform interval queries on an indexed fasta file

• Host: GitHub
• URL: https://github.com/noamteyssier/faiquery
• Owner: noamteyssier
• License: mit
• Created: 2023-08-22T17:50:38.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2023-08-23T18:39:15.000Z (almost 3 years ago)
• Last Synced: 2025-12-14T02:27:19.823Z (7 months ago)
• Topics: fai, fasta, indexed-fasta, query
• Language: Rust
• Homepage:
• Size: 17.6 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# faiquery

[![MIT licensed](https://img.shields.io/badge/license-MIT-blue.svg)](./LICENSE.md)

![actions status](https://github.com/noamteyssier/faiquery/workflows/CI/badge.svg)

[![docs.rs](https://img.shields.io/docsrs/faiquery?color=green&label=docs.rs)](https://docs.rs/faiquery/latest/faiquery/)

perform interval queries on an indexed fasta file

## Description

This is a simple utility library to request interval queries

on an indexed fasta file.

Ths index is assumed [`samtools faidx`](http://www.htslib.org/doc/samtools-faidx.html).

The fasta file is memory-mapped and a single mutable buffer is kept

for the indexed fasta reader.

This buffer is used to return a slice reference to the query sequence

but allows for a non-contiguous sequence (i.e. can return sequences without newlines)

Note that because a mutable buffer is kept, this is not the best approach for

concurrent operations.

However, for single-threaded applications, this performs very well with low memory

overhead and runtime.

## Usage

```rust

use anyhow::Result;

use faiquery::{FastaIndex, IndexedFasta};

fn main() -> Result<()> {

    let index = FastaIndex::from_filepath("example_data/example.fa.fai")?;

    let mut faidx = IndexedFasta::new(index, "example_data/example.fa")?;

    // Query the first 10 bases of chr1

    let seq = faidx.query("chr1", 0, 10)?;

    assert_eq!(seq, b"ACCTACGATC");

    // Query the first 10 bases of chr2

    let seq = faidx.query("chr2", 0, 10)?;

    assert_eq!(seq, b"TTTTGATCGA");

    Ok(())

}

```

## Similar Approaches

There are other index fasta readers that are available,

here is a nonexhaustive list of those:

- [faimm](https://crates.io/crates/faimm)

- [noodles](https://crates.io/crates/noodles)

- [rust-bio](https://crates.io/crates/bio)

If you are looking for a powerful concurrent reader I recommend

using the [faimm](https://crates.io/crates/faimm) crate.